A rapid and accurate method for determining alkaloids from Coptis chinensis Franch, and Phellodendron amurense Rupr, decocted together in Baitouweng decocta was established. Experiments were carried out on a self-assembled capillary electrophoresis system. The experimental conditions were as follows: 75 microns i.d. x 50 cm fused silica capillary, 0.05 mol/L Na2B4O7-CH3OH (85:15, V/V) as buffer, applied voltage 14 kV and detection wavelength 232 nm. In addition, the concentration of ethanol in the extraction solvent was optimized. Experimental results showed that ethanol-water (30:70, V/V) was the ideal solvent to extract the main effective ingredients from Coptis chinensis Franch. and Phellodendron amurense Rupr. decocted together in Baitouweng decocta. Berberine and palmatine had good linearities in the range of 15.0 mg/L-65.0 mg/L and 12.5 mg/L-50.0 mg/L respectively, and their average recoveries were 95.5%-104% (RSD 2.7%-6.9%) and 92.1%-103% (RSD 4.5%-6.7%) respectively.